Purpose:
Runs survival analysis models using splicing cluster assignment and 1) single exon splicing burden index (SBI) 2) KEGG Spliceosome GSVA scores or 3) CLK1 exon 4 TPM as a predictor
Uses a wrapper function (survival_analysis) from utils
folder.
Load packages, set directory paths and call setup script
library(tidyverse)
── Attaching core tidyverse packages ──────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.6
✔ forcats 1.0.1 ✔ stringr 1.6.0
✔ ggplot2 4.0.1 ✔ tibble 3.3.0
✔ lubridate 1.9.4 ✔ tidyr 1.3.1
✔ purrr 1.2.0
── Conflicts ────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(survival)
library(ggpubr)
library(ggplot2)
library(patchwork)
root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
data_dir <- file.path(root_dir, "data")
analysis_dir <- file.path(root_dir, "analyses", "survival")
input_dir <- file.path(analysis_dir, "results")
results_dir <- file.path(analysis_dir, "results")
plot_dir <- file.path(analysis_dir, "plots")
# If the input and results directories do not exist, create it
if (!dir.exists(results_dir)) {
dir.create(results_dir, recursive = TRUE)
}
source(file.path(analysis_dir, "util", "survival_models.R"))
Attaching package: 'survminer'
The following object is masked from 'package:survival':
myeloma
knitr::opts_chunk$set(cache = FALSE)
Set metadata and cluster assignment file paths
metadata_file <- file.path(input_dir, "splicing_indices_with_survival.tsv")
cluster_file <- file.path(root_dir, "analyses",
"sample-psi-clustering", "results",
"sample-cluster-metadata-top-5000-events-stranded.tsv")
kegg_scores_stranded_file <- file.path(root_dir, "analyses",
"sample-psi-clustering", "results",
"gsva_output_stranded.tsv")
tpm_file <- file.path(data_dir, "rna-isoform-expression-rsem-tpm.rds")
clk1_psi_file <- file.path(root_dir,
"analyses",
"CLK1-splicing_correlations",
"results",
"clk1-exon4-psi.tsv")
Wrangle data Add cluster assignment and spliceosome gsva scores to
metadata and define column lgg_group (LGG or
non_LGG)
metadata <- read_tsv(metadata_file)
Rows: 684 Columns: 22
── Column specification ────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (11): Kids_First_Biospecimen_ID, Histology, Kids_First_Participant_ID, m...
dbl (11): Total, AS_neg, AS_pos, AS_total, SI_Total, EFS_days, OS_days, age_...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
clusters <- read_tsv(cluster_file) %>%
dplyr::rename(Kids_First_Biospecimen_ID = sample_id)
Rows: 729 Columns: 8
── Column specification ────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (6): sample_id, plot_group, plot_group_hex, RNA_library, molecular_subty...
dbl (2): cluster, group_n
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
clk1_psi <- read_tsv(clk1_psi_file) %>%
dplyr::rename(CLK1_ex4_PSI = PSI) %>%
select(-plot_group)
Rows: 729 Columns: 3
── Column specification ────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (2): Kids_First_Biospecimen_ID, plot_group
dbl (1): PSI
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
gsva_scores <- read_tsv(kegg_scores_stranded_file) %>%
dplyr::filter(geneset == "KEGG_SPLICEOSOME") %>%
dplyr::rename(spliceosome_gsva_score = score)
Rows: 22599 Columns: 3
── Column specification ────────────────────────────────────────────────────────────────────────────────
Delimiter: "\t"
chr (2): sample_id, geneset
dbl (1): score
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
all_clk4_transcr_counts <- readRDS(tpm_file) %>%
filter(grepl("^CLK1", gene_symbol)) %>%
mutate(
transcript_id = case_when(
transcript_id %in% c("ENST00000321356.9", "ENST00000434813.3", "ENST00000409403.6") ~ "Exon 4",
# transcript_id == "ENST00000321356.9" ~ "Exon 4",
TRUE ~ "Other"
)
) %>%
group_by(transcript_id) %>%
summarise(across(starts_with("BS"), sum, na.rm = TRUE)) %>%
pivot_longer(cols = -transcript_id, names_to = "Kids_First_Biospecimen_ID", values_to = "CLK1_Ex4_TPM") %>%
filter(transcript_id == "Exon 4") %>%
inner_join(clusters, by = "Kids_First_Biospecimen_ID") %>%
left_join(clk1_psi)
Warning: There was 1 warning in `summarise()`.
ℹ In argument: `across(starts_with("BS"), sum, na.rm = TRUE)`.
ℹ In group 1: `transcript_id = "Exon 4"`.
Caused by warning:
! The `...` argument of `across()` is deprecated as of dplyr 1.1.0.
Supply arguments directly to `.fns` through an anonymous function instead.
# Previously
across(a:b, mean, na.rm = TRUE)
# Now
across(a:b, \(x) mean(x, na.rm = TRUE))
Joining with `by = join_by(Kids_First_Biospecimen_ID)`
# how many clusters?
n_clust <- length(unique(clusters$cluster))
metadata <- metadata %>%
right_join(all_clk4_transcr_counts %>% dplyr::select(Kids_First_Biospecimen_ID,
cluster, CLK1_Ex4_TPM, CLK1_ex4_PSI)) %>%
left_join(gsva_scores %>% dplyr::select(sample_id,
spliceosome_gsva_score),
by = c("Kids_First_Biospecimen_ID" = "sample_id")) %>%
dplyr::mutate(cluster = glue::glue("Cluster {cluster}")) %>%
# dplyr::mutate(cluster = fct_relevel(cluster,
# paste0("Cluster ", 1:n_clust))) %>%
dplyr::mutate(cluster = forcats::fct_relevel(cluster, "Cluster 6", after = 0)) %>%
dplyr::mutate(lgg_group = case_when(
plot_group == "Low-grade glioma" ~ "LGG",
TRUE ~ "non-LGG"
)) %>%
dplyr::mutate(SBI = SI_Total * 10) %>%
dplyr::mutate(age_at_diagnosis_years = age_at_diagnosis_days/365.25)
Joining with `by = join_by(Kids_First_Biospecimen_ID)`
Generate coxph models including extent of tumor resection, lgg group, cluster assignment, SBI, and CLK1 exon 4 TPM as covariates
add_model_os <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+SBI+CLK1_Ex4_TPM",
file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_SBI_CLK1_Ex4_TPM.RDS"),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
forest_os <- plotForest(readRDS(file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_SBI_CLK1_Ex4_TPM.RDS")))
Warning: `geom_errorbarh()` was deprecated in ggplot2 4.0.0.
ℹ Please use the `orientation` argument of `geom_errorbar()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the ggpubr package.
Please report the issue at <https://github.com/kassambara/ggpubr/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the ggpubr package.
Please report the issue at <https://github.com/kassambara/ggpubr/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
`height` was translated to `width`.
Warning: The `guide` argument in `scale_*()` cannot be `FALSE`. This was deprecated in ggplot2 3.3.4.
ℹ Please use "none" instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_os
ggsave(file.path(plot_dir, "forest_add_OS_resection_lgg_group_cluster_assignment_SBI_CLK1_Ex4_TPM.pdf"),
forest_os,
width = 10, height = 6, units = "in",
device = "pdf")
add_model_efs <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+SBI+CLK1_Ex4_TPM",
file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_SBI_CLK1_Ex4_TPM.RDS"),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_efs <- plotForest(readRDS(file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_SBI_CLK1_Ex4_TPM.RDS")))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_efs
ggsave(file.path(plot_dir, "forest_add_EFS_resection_lgg_group_cluster_assignment_SBI_CLK1_Ex4_TPM.pdf"),
forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
repeat analysis with CLK1 exon 4 TPM alone
add_model_os <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+CLK1_Ex4_TPM",
file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_CLK1_Ex4_TPM.RDS"),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
forest_os <- plotForest(readRDS(file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_CLK1_Ex4_TPM.RDS")))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_os
ggsave(file.path(plot_dir, "forest_add_OS_resection_lgg_group_cluster_assignment_CLK1_Ex4_TPM.pdf"),
forest_os,
width = 10, height = 6, units = "in",
device = "pdf")
add_model_efs <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+CLK1_Ex4_TPM",
file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_CLK1_Ex4_TPM.RDS"),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_efs <- plotForest(readRDS(file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_CLK1_Ex4_TPM.RDS")))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_efs
ggsave(file.path(plot_dir, "forest_add_EFS_resection_lgg_group_cluster_assignment_CLK1_Ex4_TPM.pdf"),
forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
repeat analysis with CLK1 exon 4 PSI
add_model_os <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+CLK1_ex4_PSI",
file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_CLK1_ex4_PSI.RDS"),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
forest_os <- plotForest(readRDS(file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_CLK1_ex4_PSI.RDS")))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_os
ggsave(file.path(plot_dir, "forest_add_OS_resection_lgg_group_cluster_assignment_CLK1_ex4_PSI.pdf"),
forest_os,
width = 10, height = 6, units = "in",
device = "pdf")
add_model_efs <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+CLK1_ex4_PSI",
file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_CLK1_ex4_PSI.RDS"),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_efs <- plotForest(readRDS(file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_CLK1_ex4_PSI.RDS")))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_efs
ggsave(file.path(plot_dir, "forest_add_EFS_resection_lgg_group_cluster_assignment_CLK1_ex4_PSI.pdf"),
forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
Interaction with GSVA, SBI, CLK1
models <- c("spliceosome_gsva_score", "SBI", "CLK1_Ex4_TPM", "CLK1_ex4_PSI")
# by cluster
for (each in models) {
int_model_efs <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = paste0("extent_of_tumor_resection+lgg_group+cluster*", each, "+age_at_diagnosis_years"),
file.path(results_dir, paste0("cox_EFS_interaction_terms_resection_lgg_group_cluster_", each, ".RDS")),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
int_forest_efs <- plotForest(readRDS(file.path(results_dir, paste0("cox_EFS_interaction_terms_resection_lgg_group_cluster_", each, ".RDS"))))
int_forest_efs
ggsave(file.path(plot_dir, paste0("forest_int_EFS_resection_lgg_group_cluster_assignment_", each, ".pdf")),
int_forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
int_model_os <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = paste0("extent_of_tumor_resection+lgg_group+cluster*", each, "+age_at_diagnosis_years"),
file.path(results_dir, paste0("cox_OS_interaction_terms_resection_lgg_group_cluster_", each, ".RDS")),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
int_forest_os <- plotForest(readRDS(file.path(results_dir, paste0("cox_OS_interaction_terms_resection_lgg_group_cluster_", each, ".RDS"))))
int_forest_os
ggsave(file.path(plot_dir, paste0("forest_int_OS_resection_lgg_group_cluster_assignment_", each, ".pdf")),
int_forest_os,
width = 10, height = 6, units = "in",
device = "pdf")
}
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
## clk1 x age
int_model_efs <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = paste0("extent_of_tumor_resection+lgg_group+cluster+CLK1_Ex4_TPM*age_at_diagnosis_years"),
file.path(results_dir, paste0("cox_EFS_interaction_terms_resection_lgg_group_cluster_CLK1_Ex4_TPM_age.RDS")),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
int_forest_efs <- plotForest(readRDS(file.path(results_dir, paste0("cox_EFS_interaction_terms_resection_lgg_group_cluster_CLK1_Ex4_TPM_age.RDS"))))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
int_forest_efs
ggsave(file.path(plot_dir, paste0("forest_int_EFS_resection_lgg_group_cluster_clk1_age.pdf")),
int_forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
int_model_os <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = paste0("extent_of_tumor_resection+lgg_group+cluster+CLK1_Ex4_TPM*age_at_diagnosis_years"),
file.path(results_dir, paste0("cox_OS_interaction_terms_resection_lgg_group_cluster_clk1_age.RDS")),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
int_forest_os <- plotForest(readRDS(file.path(results_dir, paste0("cox_OS_interaction_terms_resection_lgg_group_cluster_clk1_age.RDS"))))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
int_forest_os
ggsave(file.path(plot_dir, paste0("forest_int_OS_resection_lgg_group_cluster_clk1_age.pdf")),
int_forest_os,
width = 10, height = 6, units = "in",
device = "pdf")
models2 <- c("SBI", "CLK1_Ex4_TPM", "CLK1_ex4_PSI")
for (each in models2) {
#### by spliceosome_gsva_score
int_model_efs <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = paste0("extent_of_tumor_resection+lgg_group+cluster+spliceosome_gsva_score*", each, "+age_at_diagnosis_years"),
file.path(results_dir, paste0("cox_EFS_interaction_terms_resection_lgg_group_cluster_spliceosome_gsva_score_", each, ".RDS")),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
int_forest_efs <- plotForest(readRDS(file.path(results_dir, paste0("cox_EFS_interaction_terms_resection_lgg_group_cluster_spliceosome_gsva_score_", each, ".RDS"))))
int_forest_efs
ggsave(file.path(plot_dir, paste0("cox_EFS_interaction_terms_resection_lgg_group_cluster_spliceosome_gsva_score_", each, ".pdf")),
int_forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
}
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
add_model_efs <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+spliceosome_gsva_score+CLK1_Ex4_TPM",
file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_spliceosome_score_CLK1_Ex4_TPM.RDS"),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_efs <- plotForest(readRDS(file.path(results_dir, "cox_EFS_additive_terms_resection_lgg_group_cluster_spliceosome_score_CLK1_Ex4_TPM.RDS")))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_efs
ggsave(file.path(plot_dir, "forest_add_EFS_resection_lgg_group_cluster_assignment_spliceosome_score_CLK1_Ex4_TPM.pdf"),
forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
add_model_os <- fit_save_model(metadata[!metadata$extent_of_tumor_resection %in% c("Not Reported", "Unavailable"),],
terms = "extent_of_tumor_resection+lgg_group+cluster+age_at_diagnosis_years+spliceosome_gsva_score+CLK1_Ex4_TPM",
file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_spliceosome_score_CLK1_Ex4_TPM.RDS"),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_os <- plotForest(readRDS(file.path(results_dir, "cox_OS_additive_terms_resection_lgg_group_cluster_spliceosome_score_CLK1_Ex4_TPM.RDS")))
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
forest_os
ggsave(file.path(plot_dir, "forest_add_OS_resection_lgg_group_cluster_assignment_spliceosome_score_CLK1_Ex4_TPM.pdf"),
forest_efs,
width = 10, height = 6, units = "in",
device = "pdf")
Filter for clusters
cluster_list <- unique(metadata$cluster)
for (each in cluster_list) {
cluster_df <- metadata %>%
dplyr::filter(cluster == each,
!is.na(EFS_days)) %>%
dplyr::mutate(CLK1_TPM_group = case_when(
CLK1_Ex4_TPM > summary(CLK1_Ex4_TPM)["3rd Qu."] ~ "High CLK1 TPM",
CLK1_Ex4_TPM < summary(CLK1_Ex4_TPM)["1st Qu."] ~ "Low CLK1 TPM",
TRUE ~ NA_character_),
CLK1_PSI_group = case_when(CLK1_ex4_PSI > summary(CLK1_ex4_PSI)["3rd Qu."] ~ "High CLK1 PSI",
CLK1_ex4_PSI < summary(CLK1_ex4_PSI)["1st Qu."] ~ "Low CLK1 PSI",
TRUE ~ NA_character_
)) %>%
dplyr::mutate(CLK1_TPM_group = fct_relevel(CLK1_TPM_group,
c("Low CLK1 TPM", "High CLK1 TPM")),
CLK1_PSI_group = fct_relevel(CLK1_PSI_group,
c("Low CLK1 PSI", "High CLK1 PSI"))) %>%
# collapse groups which do not have min N
dplyr::mutate(
plot_group = forcats::fct_drop(plot_group),
plot_group = forcats::fct_lump_min(plot_group, min = 3, other_level = "Collapsed")
)
safe_each <- gsub("[^A-Za-z0-9_-]+", "_", each)
# Generate KM models with `CLK1_TPM_group` as covariate
# Generate kaplan meier survival models for OS and EFS, and save outputs
cluster_clk_tpm_kap_os <- survival_analysis(
metadata = cluster_df %>%
dplyr::filter(!is.na(CLK1_TPM_group)),
ind_var = "CLK1_TPM_group",
test = "kap.meier",
metadata_sample_col = "Kids_First_Biospecimen_ID",
days_col = "OS_days",
status_col = "OS_status"
)
readr::write_rds(cluster_clk_tpm_kap_os,
file.path(results_dir, paste0( "logrank_", safe_each, "_OS_clk1_tpm_group.RDS")))
cluster_clk_tpm_kap_efs <- survival_analysis(
metadata = cluster_df %>%
dplyr::filter(!is.na(CLK1_TPM_group)),
ind_var = "CLK1_TPM_group",
test = "kap.meier",
metadata_sample_col = "Kids_First_Biospecimen_ID",
days_col = "EFS_days",
status_col = "EFS_status"
)
readr::write_rds(cluster_clk_tpm_kap_efs,
file.path(results_dir, paste0( "logrank_", safe_each, "_EFS_clk1_tpm_group.RDS")))
# Generate KM models with `CLK1_PSI_group` as covariate
# Generate kaplan meier survival models for OS and EFS, and save outputs
cluster_clk_psi_kap_os <- survival_analysis(
metadata = cluster_df %>%
dplyr::filter(!is.na(CLK1_PSI_group)),
ind_var = "CLK1_PSI_group",
test = "kap.meier",
metadata_sample_col = "Kids_First_Biospecimen_ID",
days_col = "OS_days",
status_col = "OS_status"
)
readr::write_rds(cluster_clk_psi_kap_os,
file.path(results_dir, paste0( "logrank_", safe_each, "_OS_clk1_psi_group.RDS")))
cluster_clk_psi_kap_efs <- survival_analysis(
metadata = cluster_df %>%
dplyr::filter(!is.na(CLK1_PSI_group)),
ind_var = "CLK1_PSI_group",
test = "kap.meier",
metadata_sample_col = "Kids_First_Biospecimen_ID",
days_col = "EFS_days",
status_col = "EFS_status"
)
readr::write_rds(cluster_clk_psi_kap_efs,
file.path(results_dir, paste0( "logrank_", safe_each, "_EFS_clk1_psi_group.RDS")))
# Generate cluster KM SI_group plots
km_cluster_clk_tpm_os_plot <- plotKM(model = cluster_clk_tpm_kap_os,
variable = "CLK1_TPM_group",
combined = F,
title = paste0(each, ", overall survival"),
p_pos = "topright")
ggsave(file.path(plot_dir, paste0("km_", safe_each, "_OS_clk1_tpm_group.pdf")),
km_cluster_clk_tpm_os_plot,
width = 8, height = 5, units = "in",
device = "pdf")
km_cluster_clk1_tpm_efs_plot <- plotKM(model = cluster_clk_tpm_kap_efs,
variable = "CLK1_TPM_group",
combined = F,
title = paste0(each, ", event-free survival"),
p_pos = "topright")
ggsave(file.path(plot_dir, paste0( "km_", safe_each, "_EFS_clk1_tpm_group.pdf")),
km_cluster_clk1_tpm_efs_plot,
width = 8, height = 5, units = "in",
device = "pdf")
km_cluster_clk1_psi_os_plot <- plotKM(model = cluster_clk_psi_kap_os,
variable = "CLK1_PSI_group",
combined = F,
title = paste0(each, ", overall survival"),
p_pos = "topright")
ggsave(file.path(plot_dir, paste0( "km_", safe_each, "_OS_clk1_psi_group.pdf")),
km_cluster_clk1_psi_os_plot,
width = 8, height = 5, units = "in",
device = "pdf")
km_cluster_clk1_psi_efs_plot <- plotKM(model = cluster_clk_psi_kap_efs,
variable = "CLK1_PSI_group",
combined = F,
title = paste0(each, ", event-free survival"),
p_pos = "topright")
ggsave(file.path(plot_dir, paste0("km_", safe_each, "_EFS_clk1_psi_group.pdf")),
km_cluster_clk1_psi_efs_plot,
width = 8, height = 5, units = "in",
device = "pdf")
# Assess EFS and OS by CLK1 TPM group in multivariate models and generate forest plots
add_model_cluster_efs <- fit_save_model(cluster_df %>%
dplyr::filter(extent_of_tumor_resection != "Unavailable",
CLK1_TPM_group %in% c("High CLK1 TPM", "Low CLK1 TPM")) %>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_TPM_group",
file.path(results_dir, paste0( "cox_EFS_additive_terms_subtype_", safe_each, "_clk1_tpm_group.RDS")),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_cluster_clk1_efs <- plotForest(readRDS(file.path(results_dir, paste0("cox_EFS_additive_terms_subtype_", safe_each, "_clk1_tpm_group.RDS"))))
ggsave(file.path(plot_dir, paste0("forest_add_EFS_", safe_each, "_histology_resection_clk1_tpm_group.pdf")),
forest_cluster_clk1_efs,
width = 9, height = 4, units = "in",
device = "pdf")
add_model_cluster_os <- fit_save_model(cluster_df %>%
dplyr::filter(!extent_of_tumor_resection %in% c("Not Reported", "Unavailable")) %>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_TPM_group",
file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_tpm_group.RDS")),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
forest_cluster_clk1_os <- plotForest(readRDS(file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_tpm_group.RDS"))))
ggsave(file.path(plot_dir, paste0( "forest_add_OS_", safe_each, "_histology_resection_clk1_tpm_group.pdf")),
forest_cluster_clk1_os,
width = 9, height = 4, units = "in",
device = "pdf")
#Assess EFS and OS by CLK1 PSI group in multivariate models and generate forest plots
add_model_cluster_efs <- fit_save_model(cluster_df %>%
dplyr::filter(extent_of_tumor_resection != "Unavailable",
CLK1_PSI_group %in% c("High CLK1 PSI", "Low CLK1 PSI"))%>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_PSI_group",
file.path(results_dir, paste0( "cox_EFS_additive_terms_subtype_", safe_each, "_clk1_psi_group.RDS")),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_cluster_clk1_efs <- plotForest(readRDS(file.path(results_dir, paste0( "cox_EFS_additive_terms_subtype_", safe_each, "_clk1_psi_group.RDS"))))
ggsave(file.path(plot_dir, paste0( "forest_add_EFS_", safe_each, "_histology_resection_clk1_psi_group.pdf")),
forest_cluster_clk1_efs,
width = 9, height = 4, units = "in",
device = "pdf")
add_model_cluster_os <- fit_save_model(cluster_df %>%
dplyr::filter(!extent_of_tumor_resection %in% c("Not Reported", "Unavailable")) %>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_PSI_group",
file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_psi_group.RDS")),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
forest_cluster_clk1_os <- plotForest(readRDS(file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_psi_group.RDS"))))
ggsave(file.path(plot_dir, paste0( "forest_add_OS_", safe_each, "_histology_resection_clk1_psi_group.pdf")),
forest_cluster_clk1_os,
width = 9, height = 4, units = "in",
device = "pdf")
# Assess EFS and OS by CLK1 ex 4 TPM in multivariate models and generate forest plots
add_model_cluster_efs <- fit_save_model(cluster_df %>%
dplyr::filter(extent_of_tumor_resection != "Unavailable") %>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_Ex4_TPM",
file.path(results_dir, paste0( "cox_EFS_additive_terms_subtype_", safe_each, "_clk1_tpm.RDS")),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_cluster_clk1_efs <- plotForest(readRDS(file.path(results_dir, paste0( "cox_EFS_additive_terms_subtype_", safe_each, "_clk1_tpm.RDS"))))
ggsave(file.path(plot_dir, paste0( "forest_add_EFS_", safe_each, "_histology_resection_clk1_tpm.pdf")),
forest_cluster_clk1_efs,
width = 9, height = 4, units = "in",
device = "pdf")
add_model_cluster_os <- fit_save_model(cluster_df %>%
dplyr::filter(!extent_of_tumor_resection %in% c("Not Reported", "Unavailable")) %>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_Ex4_TPM",
file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_tpm.RDS")),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
forest_cluster_clk1_os <- plotForest(readRDS(file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_tpm.RDS"))))
ggsave(file.path(plot_dir, paste0( "forest_add_OS_", safe_each, "_histology_resection_clk1_tpm.pdf")),
forest_cluster_clk1_os,
width = 9, height = 4, units = "in",
device = "pdf")
# Assess EFS and OS by CLK1 ex 4 PSI in multivariate models and generate forest plots
add_model_cluster_efs <- fit_save_model(cluster_df %>%
dplyr::filter(extent_of_tumor_resection != "Unavailable") %>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_ex4_PSI",
file.path(results_dir, paste0( "cox_EFS_additive_terms_subtype_", safe_each, "_clk1_psi.RDS")),
"multivariate",
years_col = "EFS_years",
status_col = "EFS_status")
forest_cluster_clk1_efs <- plotForest(readRDS(file.path(results_dir, paste0( "cox_EFS_additive_terms_subtype_", safe_each, "_clk1_psi.RDS"))))
ggsave(file.path(plot_dir, paste0( "forest_add_EFS_", safe_each, "_histology_resection_clk1_psi.pdf")),
forest_cluster_clk1_efs,
width = 9, height = 4, units = "in",
device = "pdf")
add_model_cluster_os <- fit_save_model(cluster_df %>%
dplyr::filter(!extent_of_tumor_resection %in% c("Not Reported", "Unavailable")) %>%
dplyr::mutate(plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)),
terms = "extent_of_tumor_resection+age_at_diagnosis_years+plot_group+CLK1_ex4_PSI",
file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_psi.RDS")),
"multivariate",
years_col = "OS_years",
status_col = "OS_status")
forest_cluster_clk1_os <- plotForest(readRDS(file.path(results_dir, paste0( "cox_OS_additive_terms_subtype_", safe_each, "_clk1_psi.RDS"))))
ggsave(file.path(plot_dir, paste0( "forest_add_OS_", each, "_histology_resection_clk1_psi.pdf")),
forest_cluster_clk1_os,
width = 9, height = 4, units = "in",
device = "pdf")
}
Warning: Using an external vector in selections was deprecated in tidyselect 1.1.0.
ℹ Please use `all_of()` or `any_of()` instead.
# Was:
data %>% select(ind_var)
# Now:
data %>% select(all_of(ind_var))
See <https://tidyselect.r-lib.org/reference/faq-external-vector.html>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the survminer package.
Please report the issue at <https://github.com/kassambara/survminer/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.
ℹ The deprecated feature was likely used in the ggpubr package.
Please report the issue at <https://github.com/kassambara/ggpubr/issues>.
This warning is displayed once every 8 hours.
Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 2 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 2,5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 2 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,4 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 2 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,4 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,4,5,6,7,8,9 ; coefficient may be infinite.
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 6,7,8 ; coefficient may be infinite.
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 6,8 ; coefficient may be infinite.
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 6,7,8 ; coefficient may be infinite.
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 6,8 ; coefficient may be infinite.
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 5,6,7 ; coefficient may be infinite.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,2,5,8 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 4,7 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 4,7 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,2,3,4,5,6,7 ; coefficient may be infinite.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,2,3,4,5,6,7 ; coefficient may be infinite.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 4,5,7 ; coefficient may be infinite.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 4,5,7,8 ; coefficient may be infinite.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 4,5,7,8 ; coefficient may be infinite.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,2 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,2,4,5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,2,4 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Loglik converged before variable 1,2,4 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 7 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 7 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_TPM_group with kap.meier
Testing model: survival::Surv(OS_days, OS_status) ~ CLK1_PSI_group with kap.meier
Testing model: survival::Surv(EFS_days, EFS_status) ~ CLK1_PSI_group with kap.meier
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's colour values.
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• fill : ""
Warning: No shared levels found between `names(values)` of the manual scale and
the data's fill values.
Ignoring unknown labels:
• colour : ""
Warning: No shared levels found between `names(values)` of the manual scale and the data's colour values.
No shared levels found between `names(values)` of the manual scale and the data's fill values.
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Ran out of iterations and did not converge
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 1,2,5 ; coefficient may be infinite.
Warning in scale_x_log10(labels = function(x) format(x, scientific = FALSE)):
log-10 transformation introduced infinite values.
`height` was translated to `width`.
Warning: Removed 3 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Warning in coxph.fit(X, Y, istrat, offset, init, control, weights = weights, :
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
Warning: There was 1 warning in `dplyr::mutate()`.
ℹ In argument: `plot_group = forcats::fct_relevel(plot_group, "Low-grade glioma", after = 0)`.
Caused by warning:
! 1 unknown level in `f`: Low-grade glioma
Loglik converged before variable 5 ; coefficient may be infinite.
`height` was translated to `width`.
Warning: Removed 2 rows containing missing values or values outside the scale
range (`geom_text()`).
sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gtools_3.9.5 survminer_0.4.9 patchwork_1.2.0 ggpubr_0.6.0
[5] survival_3.7-0 lubridate_1.9.4 forcats_1.0.1 stringr_1.6.0
[9] dplyr_1.1.4 purrr_1.2.0 readr_2.1.6 tidyr_1.3.1
[13] tibble_3.3.0 ggplot2_4.0.1 tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] gtable_0.3.6 xfun_0.54 bslib_0.9.0 rstatix_0.7.2
[5] lattice_0.22-7 tzdb_0.5.0 vctrs_0.6.5 tools_4.4.0
[9] generics_0.1.4 parallel_4.4.0 pkgconfig_2.0.3 Matrix_1.7-4
[13] data.table_1.17.8 RColorBrewer_1.1-3 S7_0.2.1 lifecycle_1.0.4
[17] compiler_4.4.0 farver_2.1.2 textshaping_1.0.4 carData_3.0-5
[21] colorblindr_0.1.0 htmltools_0.5.8.1 sass_0.4.10 yaml_2.3.10
[25] crayon_1.5.3 pillar_1.11.1 car_3.1-2 jquerylib_0.1.4
[29] cachem_1.1.0 abind_1.4-5 km.ci_0.5-6 commonmark_2.0.0
[33] tidyselect_1.2.1 digest_0.6.39 stringi_1.8.7 labeling_0.4.3
[37] splines_4.4.0 cowplot_1.1.3 rprojroot_2.1.1 fastmap_1.2.0
[41] grid_4.4.0 colorspace_2.1-2 cli_3.6.5 magrittr_2.0.4
[45] broom_1.0.10 withr_3.0.2 scales_1.4.0 backports_1.5.0
[49] bit64_4.6.0-1 timechange_0.3.0 rmarkdown_2.30 ggtext_0.1.2
[53] bit_4.6.0 gridExtra_2.3 ggsignif_0.6.4 ragg_1.5.0
[57] zoo_1.8-12 hms_1.1.4 evaluate_1.0.5 knitr_1.50
[61] KMsurv_0.1-5 markdown_1.13 survMisc_0.5.6 rlang_1.1.6
[65] Rcpp_1.1.0 gridtext_0.1.5 xtable_1.8-4 glue_1.8.0
[69] xml2_1.5.0 vroom_1.6.6 jsonlite_2.0.0 R6_2.6.1
[73] systemfonts_1.3.1